--- trunk/OOPSE/libmdtools/DUFF.cpp 2003/06/24 19:57:54 564 +++ trunk/OOPSE/libmdtools/DUFF.cpp 2003/10/28 16:03:37 829 @@ -1,6 +1,6 @@ -#include -#include -#include +#include +#include +#include #include using namespace std; @@ -22,7 +22,7 @@ using namespace std; #define HARMONIC_BOND 1 -namespace TPE { // restrict the access of the folowing to this file only. +namespace DUFF_NS { // restrict the access of the folowing to this file only. // Declare the structures that will be passed by MPI @@ -35,6 +35,11 @@ namespace TPE { // restrict the access of the folowin double dipole; double w0; double v0; + double v0p; + double rl; + double ru; + double rlp; + double rup; int isSSD; int isDipole; int ident; @@ -138,6 +143,11 @@ namespace TPE { // restrict the access of the folowin next->dipole = info.dipole; next->w0 = info.w0; next->v0 = info.v0; + next->v0p = info.v0p; + next->rl = info.rl; + next->ru = info.ru; + next->rlp = info.rlp; + next->rup = info.rup; next->ident = info.ident; } } @@ -154,6 +164,11 @@ namespace TPE { // restrict the access of the folowin info.dipole = dipole; info.w0 = w0; info.v0 = v0; + info.v0p = v0p; + info.rl = rl; + info.ru = ru; + info.rlp = rlp; + info.rup = rup; info.ident = ident; info.last = 0; } @@ -170,6 +185,11 @@ namespace TPE { // restrict the access of the folowin double dipole; double w0; double v0; + double v0p; + double rl; + double ru; + double rlp; + double rup; int ident; LinkedAtomType* next; }; @@ -420,7 +440,7 @@ namespace TPE { // restrict the access of the folowin } // namespace -using namespace TPE; +using namespace DUFF_NS; //**************************************************************** @@ -434,7 +454,6 @@ DUFF::DUFF(){ char* ffPath_env = "FORCE_PARAM_PATH"; char* ffPath; char temp[200]; - char errMsg[1000]; headAtomType = NULL; currentAtomType = NULL; @@ -456,7 +475,7 @@ DUFF::DUFF(){ // Init the atomStruct mpi type atomStruct atomProto; // mpiPrototype - int atomBC[3] = {15,6,4}; // block counts + int atomBC[3] = {15,11,4}; // block counts MPI_Aint atomDspls[3]; // displacements MPI_Datatype atomMbrTypes[3]; // member mpi types @@ -638,12 +657,7 @@ void DUFF::readParams( void ){ void DUFF::readParams( void ){ - int i, a, b, c, d; int identNum; - char* atomA; - char* atomB; - char* atomC; - char* atomD; atomStruct atomInfo; bondStruct bondInfo; @@ -764,16 +778,18 @@ void DUFF::readParams( void ){ int isGB = 0; int isLJ = 1; - double GB_dummy = 0.0; - - + int isEAM =0; + currentAtomType = headAtomType->next;; while( currentAtomType != NULL ){ if(currentAtomType->isDipole) entry_plug->useDipole = 1; if(currentAtomType->isSSD) { entry_plug->useSticky = 1; - set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0)); + set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0), + &(currentAtomType->v0p), + &(currentAtomType->rl), &(currentAtomType->ru), + &(currentAtomType->rlp), &(currentAtomType->rup)); } if( currentAtomType->name[0] != '\0' ){ @@ -783,6 +799,7 @@ void DUFF::readParams( void ){ &(currentAtomType->isSSD), &(currentAtomType->isDipole), &isGB, + &isEAM, &(currentAtomType->epslon), &(currentAtomType->sigma), &(currentAtomType->dipole), @@ -1285,7 +1302,8 @@ void DUFF::initializeBends( int nBends, Bend** bendArr } gBend = new GhostBend( *the_atoms[a], - *the_atoms[b] ); + *the_atoms[b]); + gBend->setConstants( currentBendType->k1, currentBendType->k2, currentBendType->k3, @@ -1301,7 +1319,7 @@ void DUFF::initializeBends( int nBends, Bend** bendArr currentBendType->k3, currentBendType->t0 ); bendArray[i] = qBend; - } + } } } } @@ -1408,7 +1426,7 @@ void DUFF::fastForward( char* stopText, char* searchOw } -int TPE::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ +int DUFF_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ char* the_token; @@ -1494,15 +1512,59 @@ int TPE::parseAtom( char *lineBuffer, int lineNum, ato } info.v0 = atof( the_token ); + if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ + sprintf( painCave.errMsg, + "Error parseing AtomTypes: line %d\n", lineNum ); + painCave.isFatal = 1; + simError(); + } + + info.v0p = atof( the_token ); + + if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ + sprintf( painCave.errMsg, + "Error parseing AtomTypes: line %d\n", lineNum ); + painCave.isFatal = 1; + simError(); + } + + info.rl = atof( the_token ); + + if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ + sprintf( painCave.errMsg, + "Error parseing AtomTypes: line %d\n", lineNum ); + painCave.isFatal = 1; + simError(); + } + + info.ru = atof( the_token ); + + if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ + sprintf( painCave.errMsg, + "Error parseing AtomTypes: line %d\n", lineNum ); + painCave.isFatal = 1; + simError(); + } + + info.rlp = atof( the_token ); + + if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ + sprintf( painCave.errMsg, + "Error parseing AtomTypes: line %d\n", lineNum ); + painCave.isFatal = 1; + simError(); + } + + info.rup = atof( the_token ); } - else info.v0 = info.w0 = 0.0; + else info.v0 = info.w0 = info.v0p = info.rl = info.ru = info.rlp = info.rup = 0.0; return 1; } else return 0; } -int TPE::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ +int DUFF_NS::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ char* the_token; char bondType[30]; @@ -1541,6 +1603,8 @@ int TPE::parseBond( char *lineBuffer, int lineNum, bon } info.d0 = atof( the_token ); + + info.k0=0.0; } else if( !strcmp( bondType, "harmonic" ) ){ info.type = HARMONIC_BOND; @@ -1567,7 +1631,7 @@ int TPE::parseBond( char *lineBuffer, int lineNum, bon else{ sprintf( painCave.errMsg, "Unknown DUFF bond type \"%s\" at line %d\n", - info.type, + bondType, lineNum ); painCave.isFatal = 1; simError(); @@ -1579,7 +1643,7 @@ int TPE::parseBond( char *lineBuffer, int lineNum, bon } -int TPE::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ +int DUFF_NS::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ char* the_token; @@ -1667,7 +1731,7 @@ int TPE::parseBend( char *lineBuffer, int lineNum, ben else return 0; } -int TPE::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ +int DUFF_NS::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ char* the_token;